Welcome to Snakecdysis documentation!

About this package

You want to wrap your best snakemake workflow to be easy install and run, Snakecdysis is for you !!!!! Tha aim of Snakecdysis is to easy-wrapped snakemake workflow as python package and then build sub-commands to manage this.

Installation

• Installation
  • Requirements
  • Install Snakecdysis PyPI package
• Snakemake to python package
  • Project structure
  • Mandatory files
    • pyproject.toml file
    • The __init__.py file
    • global_variables.py file
    • main.py file
    • module.py file
    • snakefile file

Package documentation

• Snakecdysis package
  • snakecdysis.cli_wrapper Module
    • Functions
      • main_wrapper
        • main_wrapper()
  • snakecdysis.snake_wrapper Module
    • Classes
      • SnakEcdysis
        • SnakEcdysis
          • SnakEcdysis.args_cluster_config
          • SnakEcdysis.args_tools_path
          • SnakEcdysis.datatest_url_files
          • SnakEcdysis.default_profile
          • SnakEcdysis.description_tool
          • SnakEcdysis.docs
          • SnakEcdysis.export_use_yaml
          • SnakEcdysis.get_active_tools_path
          • SnakEcdysis.git_config_path
          • SnakEcdysis.git_tools_path
          • SnakEcdysis.git_url
          • SnakEcdysis.install_mode
          • SnakEcdysis.install_path
          • SnakEcdysis.latest_version
          • SnakEcdysis.singularity_url_files
          • SnakEcdysis.snakecdysis_version
          • SnakEcdysis.snakefile
          • SnakEcdysis.snakemake_scripts
          • SnakEcdysis.soft_name
          • SnakEcdysis.string_to_dag
          • SnakEcdysis.tools_mode
          • SnakEcdysis.user_cluster_config
          • SnakEcdysis.user_tools_path
          • SnakEcdysis.version
          • SnakEcdysis.check_and_download_singularity()
          • SnakEcdysis.clean_home()
          • SnakEcdysis.create_bash_completion()
          • SnakEcdysis.fail()
          • SnakEcdysis.get_config_value()
          • SnakEcdysis.get_last_version()
          • SnakEcdysis.get_tool_configfile()
          • SnakEcdysis.set_config_value()
          • SnakEcdysis.tools_version_to_df()
          • SnakEcdysis.write_config()
          • SnakEcdysis.write_user_tools_path()
      • SnakeInstaller
        • SnakeInstaller
          • SnakeInstaller.args_cluster_config
          • SnakeInstaller.args_tools_path
          • SnakeInstaller.datatest_url_files
          • SnakeInstaller.default_profile
          • SnakeInstaller.description_tool
          • SnakeInstaller.docs
          • SnakeInstaller.get_active_tools_path
          • SnakeInstaller.git_config_path
          • SnakeInstaller.git_tools_path
          • SnakeInstaller.git_url
          • SnakeInstaller.install_mode
          • SnakeInstaller.install_path
          • SnakeInstaller.latest_version
          • SnakeInstaller.singularity_url_files
          • SnakeInstaller.snakecdysis_version
          • SnakeInstaller.snakefile
          • SnakeInstaller.snakemake_scripts
          • SnakeInstaller.soft_name
          • SnakeInstaller.tools_mode
          • SnakeInstaller.user_cluster_config
          • SnakeInstaller.user_tools_path
          • SnakeInstaller.version
          • SnakeInstaller.check_and_download_singularity()
          • SnakeInstaller.clean_home()
          • SnakeInstaller.create_bash_completion()
          • SnakeInstaller.fail()
          • SnakeInstaller.get_last_version()
          • SnakeInstaller.get_tool_configfile()
          • SnakeInstaller.tools_version_to_df()
          • SnakeInstaller.write_user_tools_path()
• Workflow functions
  • Install Module

Useful functions

• Usefull functions
  • snakecdysis.useful_function Module
    • Functions
      • check_privileges
      • convert_genome_size
      • download_url
      • get_dir
      • get_files_ext
      • get_files_ext2
      • multiprocessing_download
      • sort_human
      • var_2_bool
    • Classes
      • DownloadProgressBar

Indices and tables

• Index

• Module Index

• Search Page